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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ), 'gf_id' => 'HOM05D001119', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001119' ), 'data_identifier' => 'HOM05D001119', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001119', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02060' => 'bna', 'A02p02070' => 'bna', 'A05p16370' => 'bna', 'A05p16380' => 'bna', 'A05p16390' => 'bna', 'A05p20710' => 'bna', 'A06p03920' => 'bna', 'A06p22600' => 'bna', 'A07p00500' => 'bna', 'A07p03190' => 'bna', 'A09p10180' => 'bna', 'A09p10190' => 'bna', 'A10p24650' => 'bna', 'A10p26510' => 'bna', 'A10p27030' => 'bna', 'Aa31LG10G4670' => 'aar', 'Aa31LG3G15970' => 'aar', 'Actinidia22353' => 'ach', 'Actinidia27203' => 'ach', 'Actinidia30219' => 'ach', 'Actinidia38244' => 'ach', 'Actinidia39661' => 'ach', 'Ah.07g208180' => 'amhyb', 'Ah.07g208510' => 'amhyb', 'Ah.16g104350' => 'amhyb', 'AL1G56150' => 'aly', 'AL1G56240' => 'aly', 'AL2G19300' => 'aly', 'AL5G23730' => 'aly', 'AL6G21840' => 'aly', 'AL6G24230' => 'aly', 'AL6G35900' => 'aly', 'Aqoxy1G03875' => 'aox', 'Aqoxy2G03219' => 'aox', 'Aqoxy2G03246' => 'aox', 'Aqoxy3G02819' => 'aox', 'Aqoxy3G02875' => 'aox', 'Aqoxy4G03145' => 'aox', 'Aqoxy4G03180' => 'aox', 'Aqoxy4G03184' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3R87N1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4KY2C7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ASV59L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6EV8K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H0EMIN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NT92JM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TW4QJ7' => 'arhy', 'AT1G49290' => 'ath', 'AT1G64870' => 'ath', 'AT3G45200' => 'ath', 'AT5G11220' => 'ath', 'AT5G13620' => 'ath', 'AT5G24355' => 'ath', 'ATR0375G001' => 'atr', 'ATR0549G001' => 'atr', 'ATR0549G002' => 'atr', 'ATR0564G012' => 'atr', 'ATR0564G312' => 'atr', 'Atru.chr12.627' => 'acertr', 'Atru.chr3.3728' => 'acertr', 'Atru.chr7.1702' => 'acertr', 'Atru.chr7.1703' => 'acertr', 'Atru.chr7.2285' => 'acertr', 'Atru.chr7.2286' => 'acertr', 'Atru.chr7.2406' => 'acertr', 'Atru.chr7.2408' => 'acertr', 'Atru.chr9.1273' => 'acertr', 'AUR62016111' => 'cqu', 'AUR62016112' => 'cqu', 'AUR62016113' => 'cqu', 'AUR62026866' => 'cqu', 'AUR62031531' => 'cqu', 'AUR62035057' => 'cqu', 'AUR62035058' => 'cqu', 'AUR62035059' => 'cqu', 'BcaB01g05347' => 'bca', 'BcaB02g08041' => 'bca', 'BcaB02g11059' => 'bca', 'BcaB04g20285' => 'bca', 'BcaB07g33684' => 'bca', 'BcaB08g37080' => 'bca', 'BcaC01g02098' => 'bca', 'BcaC04g19091' => 'bca', 'BcaC04g19092' => 'bca', 'BcaC04g19251' => 'bca', 'BcaC04g23108' => 'bca', 'BcaC05g27504' => 'bca', 'BcaC05g27510' => 'bca', 'BcaC06g36315' => 'bca', 'BcaC06g36702' => 'bca', 'BcaC08g44325' => 'bca', 'BcaNung05087' => 'bca', 'BcaNung05088' => 'bca', 'BcaNung06130' => 'bca', 'BcaNung06131' => 'bca', 'BolC2t06573H' => 'bol', 'BolC2t06574H' => 'bol', 'BolC3t19109H' => 'bol', 'BolC5t32200H' => 'bol', 'BolC5t32206H' => 'bol', 'BolC6t35531H' => 'bol', 'BolC6t36944H' => 'bol', 'BolC7t40531H' => 'bol', 'BolC7t40947H' => 'bol', 'BolC9t54097H' => 'bol', 'BolC9t59192H' => 'bol', 'BolC9t59389H' => 'bol', 'BolC9t59453H' => 'bol', 'BraA02t05178Z' => 'bra', 'BraA02t05179Z' => 'bra', 'BraA05t20545Z' => 'bra', 'BraA05t20546Z' => 'bra', 'BraA05t20547Z' => 'bra', 'BraA05t20978Z' => 'bra', 'BraA06t23600Z' => 'bra', 'BraA06t25334Z' => 'bra', 'BraA07t27843Z' => 'bra', 'BraA07t28116Z' => 'bra', 'BraA09t36664Z' => 'bra', 'BraA10t44528Z' => 'bra', 'BraA10t44708Z' => 'bra', 'BraA10t44754Z' => 'bra', 'C02p06290' => 'bna', 'C02p06310' => 'bna', 'C03p68500' => 'bna', 'C05p34710' => 'bna', 'C05p34780' => 'bna', 'C06p03980' => 'bna', 'C06p17500' => 'bna', 'C07p00950' => 'bna', 'C07p05470' => 'bna', 'C09p12070' => 'bna', 'C09p63460' => 'bna', 'C09p65660' => 'bna', 'C09p66720' => 'bna', 'CAN.G925.5' => 'can', 'CANSAT56G3826' => 'cansat', 'CARHR039270' => 'chi', 'CARHR039280' => 'chi', 'CARHR118190' => 'chi', 'CARHR128090' => 'chi', 'CARHR184010' => 'chi', 'CARHR199820' => 'chi', 'CARHR288970' => 'chi', 'Carub.0001s3846' => 'cru', 'Carub.0005s1099' => 'cru', 'Carub.0006s0969' => 'cru', 'Carub.0006s1178' => 'cru', 'Ca_18771_v3' => 'car', 'Ca_21322_v3' => 'car', 'Ca_27106_v3' => 'car', 'Cc06_g12150' => 'ccan', 'Cc08_g00820' => 'ccan', 'Cc08_g12150' => 'ccan', 'Cc09_g02580' => 'ccan', 'Cc09_g02590' => 'ccan', 'CDE02G4634' => 'cde', 'CDE07G0222' => 'cde', 'CDE08G0910' => 'cde', 'CDE09G1145' => 'cde', 'CDE11G0606' => 'cde', 'CDE11G0681' => 'cde', 'Cfa001587' => 'cfa', 'Cfa002990' => 'cfa', 'Cfa011109' => 'cfa', 'Cfa013160' => 'cfa', 'Ciclev10003740m.g' => 'ccl', 'Ciclev10010600m.g' => 'ccl', 'Ciclev10023055m.g' => 'ccl', 'Ciclev10024012m.g' => 'ccl', 'Ciclev10029977m.g' => 'ccl', 'Ciclev10030277m.g' => 'ccl', 'Ciclev10030298m.g' => 'ccl', 'Ciclev10033619m.g' => 'ccl', 'CiPaw.01G277000' => 'cil', 'CiPaw.03G206700' => 'cil', 'CiPaw.07G222000' => 'cil', 'CiPaw.13G029000' => 'cil', 'ClCG03G015090' => 'cla', 'ClCG05G000350' => 'cla', 'ClCG08G013300' => 'cla', 'ClCG09G020410' => 'cla', 'COL.COLO4_12441' => 'col', 'COL.COLO4_18099' => 'col', 'COL.COLO4_18841' => 'col', 'COL.COLO4_37121' => 'col', 'Cpa.g.c32489.1' => 'cpa', 'Cpa.g.c32489.2' => 'cpa', 'Cpa.g.sc1.267' => 'cpa', 'Cpa.g.sc115.1' => 'cpa', 'Cpa.g.sc259.10' => 'cpa', 'Cpa.g.sc259.8' => 'cpa', 'Cpa.g.sc259.9' => 'cpa', 'Cpa.g.sc28.41' => 'cpa', 'CsaV3_1G041020' => 'csa', 'CsaV3_2G032020' => 'csa', 'CsaV3_3G007510' => 'csa', 'CsaV3_5G026010' => 'csa', 'CSS0011228' => 'camsi', 'CSS0033842' => 'camsi', 'CSS0035501' => 'camsi', 'CSS0049036' => 'camsi', 'Dinv21658' => 'din', 'Dinv30150' => 'din', 'Dinv31363' => 'din', 'Dinv31365' => 'din', 'Dinv42392' => 'din', 'Dinv44083' => 'din', 'Duzib128G1698' => 'dzi', 'Duzib150G1609' => 'dzi', 'Duzib168G2357' => 'dzi', 'Duzib187G1631' => 'dzi', 'Duzib205G1334' => 'dzi', 'ECA232G2364' => 'eca', 'ECA247G3237' => 'eca', 'EL10Ac2g04202' => 'bvu', 'EL10Ac2g04242' => 'bvu', 'EL10Ac3g05802' => 'bvu', 'EL10Ac3g05803' => 'bvu', 'Eucgr.C00815' => 'egr', 'Eucgr.G02794' => 'egr', 'FAN01G1664' => 'fan', 'FAN03G1298' => 'fan', 'FAN03G1394' => 'fan', 'FAN03G3226' => 'fan', 'FAN06G2550' => 'fan', 'FAN06G4087' => 'fan', 'FAN10G0839' => 'fan', 'FAN10G2844' => 'fan', 'FAN10G2964' => 'fan', 'FAN10G3081' => 'fan', 'FAN15G0351' => 'fan', 'FAN15G0903' => 'fan', 'FAN16G1566' => 'fan', 'FAN19G1768' => 'fan', 'FAN20G1116' => 'fan', 'FAN21G3374' => 'fan', 'FAN23G2811' => 'fan', 'FAN24G2291' => 'fan', 'FAN24G2681' => 'fan', 'FAN26G0450' => 'fan', 'FAN26G2421' => 'fan', 'FAN27G2031' => 'fan', 'FAN28G0016' => 'fan', 'FvH4_1g08631' => 'fve', 'FvH4_2g11491' => 'fve', 'FvH4_2g29280' => 'fve', 'FvH4_3g26240' => 'fve', 'FvH4_3g33792' => 'fve', 'FvH4_7g09600' => 'fve', 'FvH4_7g20310' => 'fve', 'FvH4_7g20311' => 'fve', 'Glyma.02G156500' => 'gma', 'Glyma.02G161566' => 'gma', 'Glyma.06G064300' => 'gma', 'Glyma.13G110400' => 'gma', 'Glyma.17G049300' => 'gma', 'Glyma.20G021800' => 'gma', 'Gohir.A07G027700' => 'ghi', 'Gohir.A07G115550' => 'ghi', 'Gohir.A08G059750' => 'ghi', 'Gohir.A08G168300' => 'ghi', 'Gohir.A13G021400' => 'ghi', 'Gohir.A13G190900' => 'ghi', 'Gohir.D07G031700' => 'ghi', 'Gohir.D07G120000' => 'ghi', 'Gohir.D08G068950' => 'ghi', 'Gohir.D08G186900' => 'ghi', 'Gohir.D13G022000' => 'ghi', 'Gohir.D13G196380' => 'ghi', 'Gorai.001G033100' => 'gra', 'Gorai.001G129200' => 'gra', 'Gorai.004G072300' => 'gra', 'Gorai.004G196600' => 'gra', 'Gorai.013G024800' => 'gra', 'Gorai.013G224400' => 'gra', 'GSVIVG01015084001' => 'vvi', 'GSVIVG01016349001' => 'vvi', 'HanXRQChr09g0247131' => 'han', 'HanXRQChr09g0247141' => 'han', 'HanXRQChr09g0247151' => 'han', 'HanXRQChr09g0247181' => 'han', 'HanXRQChr15g0496811' => 'han', 'Haze_02761' => 'cav', 'Haze_16943' => 'cav', 'Haze_26011' => 'cav', 'Hma1.2p1_0169F.1_g074540' => 'hma', 'Hma1.2p1_0179F.1_g079540' => 'hma', 'Hma1.2p1_0192F.1_g083540' => 'hma', 'Hma1.2p1_1740F.1_g300080' => 'hma', 'HPP92_002670' => 'vpl', 'HPP92_002723' => 'vpl', 'HPP92_025601' => 'vpl', 'HPP92_025614' => 'vpl', 'HPP92_025641' => 'vpl', 'Lalb_Chr03g0036451' => 'lal', 'Lalb_Chr04g0252291' => 'lal', 'Lalb_Chr08g0244021' => 'lal', 'Lalb_Chr12g0200141' => 'lal', 'Lalb_Chr13g0299451' => 'lal', 'Lalb_Chr19g0129081' => 'lal', 'Lalb_Chr19g0129091' => 'lal', 'Lalb_Chr23g0268591' => 'lal', 'Lj1A925T63' => 'lonja', 'Lj1g0000301' => 'lja', 'Lj1g0024903' => 'lja', 'Lj2g0016450' => 'lja', 'Lj3g0002278' => 'lja', 'Lj3g0021803' => 'lja', 'Lj3g0022883' => 'lja', 'Lj4C912T8' => 'lonja', 'Lj4g0006473' => 'lja', 'Lj4g0012074' => 'lja', 'Lj4g0017342' => 'lja', 'Lj4g0023093' => 'lja', 'Lj4g0025779' => 'lja', 'Lj5g0014110' => 'lja', 'Lj7A541G77' => 'lonja', 'Lsat_1_v5_gn_1_22961' => 'lsa', 'Lsat_1_v5_gn_9_66661' => 'lsa', 'Manes.01G083500' => 'mes', 'Manes.01G271400' => 'mes', 'Manes.10G041300' => 'mes', 'Manes.16G095400' => 'mes', 'Manes.16G121000' => 'mes', 'MBI04_g34407_MAGBIO' => 'mbi', 'MBI11_g20526_MAGBIO' => 'mbi', 'MD02G1091200' => 'mdo', 'MD03G1108800' => 'mdo', 'MD07G1100200' => 'mdo', 'MD07G1180400' => 'mdo', 'MD08G1149000' => 'mdo', 'MD11G1122600' => 'mdo', 'MD15G1124100' => 'mdo', 'MD15G1217400' => 'mdo', 'Medtr1g008070' => 'mtr', 'Medtr1g008090' => 'mtr', 'Medtr1g046710' => 'mtr', 'Medtr1g048380' => 'mtr', 'Medtr1g102760' => 'mtr', 'Medtr2g095470' => 'mtr', 'Medtr3g107400' => 'mtr', 'Medtr4g083770' => 'mtr', 'Medtr4g125340' => 'mtr', 'Medtr4g125350' => 'mtr', 'Medtr7g032860' => 'mtr', 'Medtr8g006200' => 'mtr', 'Medtr8g045370' => 'mtr', 'Medtr8g045420' => 'mtr', 'MELO3C005973.2' => 'cme', 'MELO3C011255.2' => 'cme', 'MELO3C015520.2' => 'cme', 'MELO3C025499.2' => 'cme', 'Migut.F01793' => 'egut', 'Migut.J00927' => 'egut', 'Migut.L01565' => 'egut', 'MSTRG.19461' => 'ama', 'Nitab4.5_0000061g0300' => 'nta', 'Nitab4.5_0000209g0080' => 'nta', 'Nitab4.5_0000268g0010' => 'nta', 'Nitab4.5_0000447g0030' => 'nta', 'Nitab4.5_0002562g0010' => 'nta', 'Nitab4.5_0002831g0010' => 'nta', 'Nitab4.5_0003582g0040' => 'nta', 'Nitab4.5_0004331g0010' => 'nta', 'Nitab4.5_0006414g0030' => 'nta', 'Nn2g10643' => 'nnu', 'Nn2g14751' => 'nnu', 'Nn2g14752' => 'nnu', 'Nn3g19892' => 'nnu', 'Nn3g19893' => 'nnu', 'Nn3g19895' => 'nnu', 'Nn6g33849' => 'nnu', 'Oeu015765.1' => 'oeu', 'Oeu017236.1' => 'oeu', 'Oeu024041.1' => 'oeu', 'Oeu024044.1' => 'oeu', 'Oeu026598.1' => 'oeu', 'Oeu037451.1' => 'oeu', 'Oeu042687.1' => 'oeu', 'Oeu051902.1' => 'oeu', 'Oeu051988.1' => 'oeu', 'Oeu057959.1' => 'oeu', 'Oeu057969.1' => 'oeu', 'Oeu063033.1' => 'oeu', 'Os07g0274300' => 'osa', 'Os10g0561000' => 'osa', 'Peaxi162Scf00073g00122' => 'pax', 'Peaxi162Scf00127g00193' => 'pax', 'Peaxi162Scf00208g00028' => 'pax', 'Peaxi162Scf00208g00083' => 'pax', 'Peaxi162Scf00377g00091' => 'pax', 'PGR044G2085' => 'pgr', 'PGR142G2693' => 'pgr', 'PGR142G3585' => 'pgr', 'PGSC0003DMG400010569' => 'stu', 'PGSC0003DMG400037534' => 'stu', 'PGSC0003DMG400046394' => 'stu', 'PGSC0003DMG400046847' => 'stu', 'PGSC0003DMG400046974' => 'stu', 'Phvul.002G099200' => 'pvu', 'Phvul.003G130800' => 'pvu', 'Phvul.004G140300' => 'pvu', 'Phvul.007G239900' => 'pvu', 'Potri.001G155600' => 'ptr', 'Potri.006G252800' => 'ptr', 'Potri.008G045000' => 'ptr', 'Potri.010G216400' => 'ptr', 'Potri.014G054900' => 'ptr', 'Prupe.1G479500' => 'ppe', 'Prupe.2G219300' => 'ppe', 'Prupe.2G219700' => 'ppe', 'Prupe.3G138200' => 'ppe', 'Prupe.6G092000' => 'ppe', 'Prupe.7G081400' => 'ppe', 'Prupe.7G199100' => 'ppe', 'Psat0s1161g0040' => 'psa', 'Psat4g017600' => 'psa', 'Psat4g098760' => 'psa', 'Psat4g226840' => 'psa', 'Psat7g131800' => 'psa', 'PSO017G2543' => 'pso', 'PSO017G5591' => 'pso', 'PSO017G7248' => 'pso', 'PSO063G1091' => 'pso', 'PSO063G1671' => 'pso', 'PSO063G3146' => 'pso', 'PSO063G5297' => 'pso', 'PSO063G7393' => 'pso', 'PSO135G0024' => 'pso', 'PSO170G1230' => 'pso', 'PSO170G1459' => 'pso', 'PSO210G0493' => 'pso', 'PSO210G6208' => 'pso', 'PSO339G2552' => 'pso', 'PSO339G3271' => 'pso', 'PSO384G0338' => 'pso', 'PSO384G1044' => 'pso', 'PSO384G1933' => 'pso', 'PSO384G1969' => 'pso', 'PSO515G0001' => 'pso', 'PSO515G0002' => 'pso', 'PSO538G0002' => 'pso', 'PSO538G0004' => 'pso', 'PSO675G1477' => 'pso', 'PSO732G0461' => 'pso', 'PSO732G0819' => 'pso', 'PSO761G0289' => 'pso', 'PSO782G4752' => 'pso', 'PSO832G0176' => 'pso', 'PSO832G0552' => 'pso', 'QL01p036392' => 'qlo', 'QL01p036396' => 'qlo', 'QL01p036403' => 'qlo', 'QL02p021952' => 'qlo', 'QL04p033568' => 'qlo', 'QL08p056978' => 'qlo', 'QL11p000714' => 'qlo', 'QL11p000739' => 'qlo', 'QL12p011372' => 'qlo', 'RcHm_v2.0_Chr1g0346521' => 'rch', 'RcHm_v2.0_Chr1g0364241' => 'rch', 'RcHm_v2.0_Chr1g0364261' => 'rch', 'RcHm_v2.0_Chr2g0094911' => 'rch', 'RcHm_v2.0_Chr5g0048831' => 'rch', 'RcHm_v2.0_Chr5g0048891' => 'rch', 'RcHm_v2.0_Chr5g0048921' => 'rch', 'RcHm_v2.0_Chr6g0270221' => 'rch', 'RcHm_v2.0_Chr6g0298091' => 'rch', 'Rhsim01G0137200' => 'rsi', 'Rhsim02G0199400' => 'rsi', 'Rhsim03G0122400' => 'rsi', 'Rhsim05G0007600' => 'rsi', 'Sabra01G0125300' => 'sbr', 'Sabra06G0197600' => 'sbr', 'Sabra08G0031200' => 'sbr', 'Sabra10G0167500' => 'sbr', 'Sabra14G0040600' => 'sbr', 'SalBow3G1740' => 'sbo', 'SalBow3G1965' => 'sbo', 'Sc18g0002540' => 'sci', 'Sc23g0001530' => 'sci', 'Sc23g0006850' => 'sci', 'Sed0006454' => 'sed', 'Sed0016988' => 'sed', 'Sed0019479' => 'sed', 'Sed0019806' => 'sed', 'Sed0023743' => 'sed', 'SGA_v2.0_scaffold308G48075' => 'sas', 'SGA_v2.0_scaffold71G24034' => 'sas', 'SHI04807' => 'shi', 'Solyc01g090540.1' => 'sly', 'Solyc04g049860.2' => 'sly', 'Solyc08g060960.1' => 'sly', 'Solyc12g020130.1' => 'sly', 'Solyc12g038130.1' => 'sly', 'Solyc12g038140.1' => 'sly', 'Sopen04g020180' => 'spe', 'Sopen12g017780' => 'spe', 'Sp1g36170' => 'spa', 'Sp6g30410' => 'spa', 'Sp7g06000' => 'spa', 'Sp7g07430' => 'spa', 'Sp7g07480' => 'spa', 'TAR383G0586' => 'tar', 'TAR633G1771' => 'tar', 'TAR633G2176' => 'tar', 'TAR633G2459' => 'tar', 'THA.LOC104799361' => 'tha', 'THA.LOC104815016' => 'tha', 'THA.LOC104817197' => 'tha', 'Thecc.01G389200' => 'tca', 'Thecc.03G248000' => 'tca', 'Thecc.09G026700' => 'tca', 'Thecc.09G077000' => 'tca', 'Thecc.09G077100' => 'tca', 'Thecc.09G262600' => 'tca', 'Thecc.10G066500' => 'tca', 'Thecc.10G066900' => 'tca', 'Thhalv10005525m.g' => 'esa', 'Thhalv10005631m.g' => 'esa', 'Thhalv10005652m.g' => 'esa', 'Thhalv10012183m.g' => 'esa', 'Thhalv10015649m.g' => 'esa', 'Thhalv10015793m.g' => 'esa', 'TPR.G12629' => 'tpr', 'TPR.G20994' => 'tpr', 'TPR.G32782' => 'tpr', 'TPR.G35690' => 'tpr', 'TPR.G35702' => 'tpr', 'TPR.G7180' => 'tpr', 'TPR.G7774' => 'tpr', 'TWI15G0565' => 'twi', 'TWI23G0964' => 'twi', 'TWI34G1834' => 'twi', 'TWI38G1075' => 'twi', 'unitig_747.g21461' => 'ugi', 'unitig_8.g3531' => 'ugi', 'vmacro11157' => 'vma', 'vmacro17200' => 'vma', 'vmacro17201' => 'vma', 'VMungo0251G2913' => 'vmu', 'VMungo0720G1859' => 'vmu', 'VMungo1215G2745' => 'vmu', 'Zm00001eb023180' => 'zma', 'Zm00001eb197450' => 'zma', 'Zm00001eb197470' => 'zma', 'Zm00001eb304880' => 'zma', 'Zm00001eb391160' => 'zma', 'Zm00001eb420590' => 'zma' ) $gf_id = 'HOM05D001119' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001119' ) $data_identifier = 'HOM05D001119' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 28, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 8, 'arhy' => (int) 7, 'ath' => (int) 6, 'atr' => (int) 5, 'acertr' => (int) 9, 'cqu' => (int) 8, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 14, 'can' => (int) 1, 'cansat' => (int) 1, 'chi' => (int) 7, 'cru' => (int) 4, 'car' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 8, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 8, 'csa' => (int) 4, 'camsi' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 5, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 2, 'fan' => (int) 23, 'fve' => (int) 8, 'gma' => (int) 6, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 12, 'lsa' => (int) 2, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 8, 'mtr' => (int) 14, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 9, 'nnu' => (int) 7, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppe' => (int) 7, 'psa' => (int) 5, 'pso' => (int) 30, 'qlo' => (int) 9, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 8, 'esa' => (int) 6, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 3, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb420590' $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